title: Reconstructing the free-energy landscape of Met-enkephalin using dihedral principal component analysis and well-tempered metadynamics.
abstract: Well-Tempered Metadynamics (WTmetaD) is an efficient method to enhance the reconstruction of the free-energy surface of proteins. WTmetaD guarantees a faster convergence in the long time limit in comparison with the standard metadynamics. It still suffers, however, from the same limitation, i.e., the non-trivial choice of pertinent collective variables (CVs). To circumvent this problem, we couple WTmetaD with a set of CVs generated from a dihedral Principal Component Analysis (dPCA) on the Ramachandran dihedral angles describing the backbone structure of the protein. The dPCA provides a generic method to extract relevant CVs built from internal coordinates, and does not depend on the alignment to an arbitrarily chosen reference structure as usual in Cartesian PCA. We illustrate the robustness of this method in the case of a reference model protein, the small and very diffusive Met-enkephalin pentapeptide. We propose a justification a posteriori of the considered number of CVs necessary to bias the metadynamics simulation in terms of the one-dimensional free-energy profiles associated with Ramachandran dihedral angles along the amino-acid sequence.
authors.affiliation: Laboratoire Interdisciplinaire Carnot de Bourgogne, UMR 6303 CNRS-Université de Bourgogne, 9 Avenue A. Savary, BP 47 870, F-21078 Dijon Cedex, France. francois.sicard@irsamc.ups-tlse.fr
authors.forename: François
authors.initials: F
authors.lastname: Sicard
authors.forename: Patrick
authors.initials: P
authors.lastname: Senet
mesh_terms: D000465:Algorithms; D003198:Computer Simulation; D004734:Energy Metabolism; D004744:Enkephalin, Methionine / Q000737:chemistry*; D025341:Principal Component Analysis; D011487:Protein Conformation; D013499:Surface Properties; D013816:Thermodynamics
chemical_list: D004744:Enkephalin, Methionine